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Ivanova OM, Anufrieva KS, Kazakova AN, Malyants IK, Shnaider PV, Lukina MM, Shender VO. Non-canonical functions of spliceosome components in cancer progression. Cell Death Dis 2023; 14:77. [PMID: 36732501 PMCID: PMC9895063 DOI: 10.1038/s41419-022-05470-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 02/04/2023]
Abstract
Dysregulation of pre-mRNA splicing is a common hallmark of cancer cells and it is associated with altered expression, localization, and mutations of the components of the splicing machinery. In the last few years, it has been elucidated that spliceosome components can also influence cellular processes in a splicing-independent manner. Here, we analyze open source data to understand the effect of the knockdown of splicing factors in human cells on the expression and splicing of genes relevant to cell proliferation, migration, cell cycle regulation, DNA repair, and cell death. We supplement this information with a comprehensive literature review of non-canonical functions of splicing factors linked to cancer progression. We also specifically discuss the involvement of splicing factors in intercellular communication and known autoregulatory mechanisms in restoring their levels in cells. Finally, we discuss strategies to target components of the spliceosome machinery that are promising for anticancer therapy. Altogether, this review greatly expands understanding of the role of spliceosome proteins in cancer progression.
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Affiliation(s)
- Olga M Ivanova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation.
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation.
- Institute for Regenerative Medicine, Sechenov University, Moscow, 119991, Russian Federation.
| | - Ksenia S Anufrieva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Anastasia N Kazakova
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, 141701, Russian Federation
| | - Irina K Malyants
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Faculty of Chemical-Pharmaceutical Technologies and Biomedical Drugs, Mendeleev University of Chemical Technology of Russia, Moscow, 125047, Russian Federation
| | - Polina V Shnaider
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russian Federation
| | - Maria M Lukina
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Victoria O Shender
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation.
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russian Federation.
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2
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Bagheri A, Astafev A, Al-Hashimy T, Jiang P. Tracing Translational Footprint by Ribo-Seq: Principle, Workflow, and Applications to Understand the Mechanism of Human Diseases. Cells 2022; 11:cells11192966. [PMID: 36230928 PMCID: PMC9562884 DOI: 10.3390/cells11192966] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/02/2022] [Accepted: 09/19/2022] [Indexed: 11/30/2022] Open
Abstract
RNA-seq has been widely used as a high-throughput method to characterize transcript dynamic changes in a broad context, such as development and diseases. However, whether RNA-seq-estimated transcriptional dynamics can be translated into protein level changes is largely unknown. Ribo-seq (Ribosome profiling) is an emerging technology that allows for the investigation of the translational footprint via profiling ribosome-bounded mRNA fragments. Ribo-seq coupled with RNA-seq will allow us to understand the transcriptional and translational control of the fundamental biological process and human diseases. This review focuses on discussing the principle, workflow, and applications of Ribo-seq to study human diseases.
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Affiliation(s)
- Atefeh Bagheri
- Department of Biological, Geological and Environmental Sciences (BGES), Cleveland State University, Cleveland, OH 44115, USA
- Center for Gene Regulation in Health and Disease (GRHD), Cleveland State University, Cleveland, OH 44115, USA
| | - Artem Astafev
- Department of Biological, Geological and Environmental Sciences (BGES), Cleveland State University, Cleveland, OH 44115, USA
- Center for Gene Regulation in Health and Disease (GRHD), Cleveland State University, Cleveland, OH 44115, USA
| | - Tara Al-Hashimy
- Department of Biological, Geological and Environmental Sciences (BGES), Cleveland State University, Cleveland, OH 44115, USA
| | - Peng Jiang
- Department of Biological, Geological and Environmental Sciences (BGES), Cleveland State University, Cleveland, OH 44115, USA
- Center for Gene Regulation in Health and Disease (GRHD), Cleveland State University, Cleveland, OH 44115, USA
- Center for Applied Data Analysis and Modeling (ADAM), Cleveland State University, Cleveland, OH 44115, USA
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Correspondence: ; Tel.: +1-(216)-687-3917
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Choo SW, Zhong Y, Sendler E, Goustin AS, Cai J, Ju D, Kosir MA, Giordo R, Lipovich L. Estrogen distinctly regulates transcription and translation of lncRNAs and pseudogenes in breast cancer cells. Genomics 2022; 114:110421. [PMID: 35779786 DOI: 10.1016/j.ygeno.2022.110421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 05/25/2022] [Accepted: 06/25/2022] [Indexed: 11/04/2022]
Abstract
Estrogen drives key transcriptional changes in breast cancer and stimulates breast cancer cells' growth with multiple mechanisms to coordinate transcription and translation. In addition to protein-coding transcripts, estrogen can regulate long non-coding RNA (lncRNA) transcripts, plus diverse non-coding RNAs including antisense, enhancer, and intergenic. LncRNA genes comprise the majority of human genes. The accidental, or regulated, translation of their short open reading frames by ribosomes remains a controversial topic. Here we report for the first time an integrated analysis of RNA abundance and ribosome occupancy level, using Ribo-seq combined with RNA-Seq, in the estrogen-responsive, estrogen receptor α positive, human breast cancer cell model MCF7, before and after hormone treatment. Translational profiling can determine, in an unbiased manner, which fraction of the genome is actually translated into proteins, as well as resolving whether transcription and translation respond concurrently, or differentially, to estrogen treatment. Our data showed specific transcripts more robustly detected in RNA-Seq than in the ribosome-profiling data, and vice versa, suggesting distinct gene-specific estrogen responses at the transcriptional and the translational level, respectively. Here, we showed that estrogen stimulation affects the expression levels of numerous lncRNAs, but not their association with ribosomes, and that most lncRNAs are not ribosome-bound. For the first time, we also demonstrated the transcriptional and translational response of expressed pseudogenes to estrogen, pointing to new perspectives for drug-target development in breast cancer in the future.
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Affiliation(s)
- Siew-Woh Choo
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, China; Zhejiang Bioinformatics International Science and Technology Cooperation Center, Ouhai, Wenzhou, Zhejiang Province, China; Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, Ouhai, Wenzhou, Zhejiang Province, China.
| | - Yu Zhong
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Edward Sendler
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, USA
| | - Anton-Scott Goustin
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, USA
| | - Juan Cai
- Department of Biochemistry, Microbiology and Immunology School of Medicine, Wayne State University, Detroit, USA
| | - Donghong Ju
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, USA; Department of Surgery and Karmanos Cancer Institute, School of Medicine, Wayne State University, Detroit, USA
| | - Mary Ann Kosir
- Department of Surgery and Karmanos Cancer Institute, School of Medicine, Wayne State University, Detroit, USA
| | - Roberta Giordo
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.
| | - Leonard Lipovich
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.
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The Clinical Role of SRSF1 Expression in Cancer: A Review of the Current Literature. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12052268] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Background: SFRS1 is a member of the splicing factor protein family. Through a specific sequence of alteration, SRSF1 can move from the cytoplasm to the nucleus where it can work autonomously as a splicing activator, or as a silencer when interacting with other regulators. Alternative splicing (AS) is a fundamental biological process that ensures protein diversity. In fact, different proteins, produced by alternative splicing, can gain different and even antagonistic biological functions. Methods: Our review is based on English articles published in the MEDLINE/PubMed medical library between 2000 and 2021. We retrieved articles that were specifically related to SRSF1 and cancers, and we excluded other reviews and meta-analyses. We included in vitro studies, animal studies and clinical studies, evaluated using the Medical Education Research Study Quality Instrument (MERSQI) and the Newcastle–Ottawa Scale-Education (NOSE). Result: SRSF1 is related to various genes and plays a role in cell cycle, ubiquitin-mediated proteolysis, nucleotide excision repair, p53 pathway, apoptosis, DNA replication and RNA degradation. In most cases, SRSF1 carries out its cancer-related function via abnormal alternative splicing (AS). However, according to the most recent literature, SRSF1 may also be involved in mRNA translation and cancer chemoresistance or radio-sensitivity. Conclusion: Our results showed that SRSF1 plays a key clinical role in tumorigenesis and tumor progression in several types of cancer (such as Prostate, Lung, Breast, Colon, Glioblastoma), through various mechanisms of action and different cellular pathways. This review could be a starting point for several studies regarding the biology of and therapies for cancer.
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Veiga DFT, Nesta A, Zhao Y, Mays AD, Huynh R, Rossi R, Wu TC, Palucka K, Anczukow O, Beck CR, Banchereau J. A comprehensive long-read isoform analysis platform and sequencing resource for breast cancer. SCIENCE ADVANCES 2022; 8:eabg6711. [PMID: 35044822 PMCID: PMC8769553 DOI: 10.1126/sciadv.abg6711] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Tumors display widespread transcriptome alterations, but the full repertoire of isoform-level alternative splicing in cancer is unknown. We developed a long-read (LR) RNA sequencing and analytical platform that identifies and annotates full-length isoforms and infers tumor-specific splicing events. Application of this platform to breast cancer samples identifies thousands of previously unannotated isoforms; ~30% affect protein coding exons and are predicted to alter protein localization and function. We performed extensive cross-validation with -omics datasets to support transcription and translation of novel isoforms. We identified 3059 breast tumor–specific splicing events, including 35 that are significantly associated with patient survival. Of these, 21 are absent from GENCODE and 10 are enriched in specific breast cancer subtypes. Together, our results demonstrate the complexity, cancer subtype specificity, and clinical relevance of previously unidentified isoforms and splicing events in breast cancer that are only annotatable by LR-seq and provide a rich resource of immuno-oncology therapeutic targets.
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Affiliation(s)
- Diogo F. T. Veiga
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | - Alex Nesta
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Yuqi Zhao
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | | | - Richie Huynh
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | - Robert Rossi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | - Te-Chia Wu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | - Karolina Palucka
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | - Olga Anczukow
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA
- Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030, USA
- Corresponding author. (O.A.); (C.R.B.); (J.B.)
| | - Christine R. Beck
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA
- Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030, USA
- Corresponding author. (O.A.); (C.R.B.); (J.B.)
| | - Jacques Banchereau
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
- Corresponding author. (O.A.); (C.R.B.); (J.B.)
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Mundodi V, Choudhary S, Smith AD, Kadosh D. Global translational landscape of the Candida albicans morphological transition. G3-GENES GENOMES GENETICS 2021; 11:6046988. [PMID: 33585865 PMCID: PMC7849906 DOI: 10.1093/g3journal/jkaa043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 12/01/2020] [Indexed: 12/14/2022]
Abstract
Candida albicans, a major human fungal pathogen associated with high mortality and/or morbidity rates in a wide variety of immunocompromised individuals, undergoes a reversible morphological transition from yeast to filamentous cells that is required for virulence. While previous studies have identified and characterized global transcriptional mechanisms important for driving this transition, as well as other virulence properties, in C. albicans and other pathogens, considerably little is known about the role of genome-wide translational mechanisms. Using ribosome profiling, we report the first global translational profile associated with C. albicans morphogenesis. Strikingly, many genes involved in pathogenesis, filamentation, and the response to stress show reduced translational efficiency (TE). Several of these genes are known to be strongly induced at the transcriptional level, suggesting that a translational fine-tuning mechanism is in place. We also identify potential upstream open reading frames (uORFs), associated with genes involved in pathogenesis, and novel ORFs, several of which show altered TE during filamentation. Using a novel bioinformatics method for global analysis of ribosome pausing that will be applicable to a wide variety of genetic systems, we demonstrate an enrichment of ribosome pausing sites in C. albicans genes associated with protein synthesis and cell wall functions. Altogether, our results suggest that the C. albicans morphological transition, and most likely additional virulence processes in fungal pathogens, is associated with widespread global alterations in TE that do not simply reflect changes in transcript levels. These alterations affect the expression of many genes associated with processes essential for virulence and pathogenesis.
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Affiliation(s)
- Vasanthakrishna Mundodi
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Saket Choudhary
- Department of Computational Biology and Bioinformatics, University of Southern California, Los Angeles, CA 90089, USA
| | - Andrew D Smith
- Department of Computational Biology and Bioinformatics, University of Southern California, Los Angeles, CA 90089, USA
| | - David Kadosh
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
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Cava C, Pini S, Taramelli D, Castiglioni I. Perturbations of pathway co-expression network identify a core network in metastatic breast cancer. Comput Biol Chem 2020; 87:107313. [PMID: 32590221 DOI: 10.1016/j.compbiolchem.2020.107313] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 04/03/2020] [Accepted: 06/18/2020] [Indexed: 12/17/2022]
Abstract
Metastases are the main cause of death in advanced breast cancer (BC) patients. Although chemotherapy and hormone therapy are current treatment strategies, drug resistance is frequent and still not completely understood. In this study, a bioinformatics analysis was performed on BC patients to explore the molecular mechanisms associated with BC metastasis. Microarray gene expression profiles of metastatic and non metastatic BC patients were downloaded from Gene Expression Omnibus (GEO) dataset. Raw data were normalized and merged using the Combat tool. Pathways enriched with differently expressed genes were identified and a pathway co-expression network was generated using Pearson's correlation. We identified from this network, which includes 17 pathways and 128 interactions, the pathways that most influence the network efficiency. Moreover, protein interaction network was investigated to identify hub genes of the pathway network. The prognostic role of the network was evaluated with a survival analysis using an independent dataset. In conclusion, the pathway co-expression network could contribute to understanding the mechanism and development of BC metastases.
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Affiliation(s)
- Claudia Cava
- Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), Via F.Cervi 93, 20090, Segrate, Milan, Italy.
| | - Simone Pini
- Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), Via F.Cervi 93, 20090, Segrate, Milan, Italy; Department of Pharmacological & Biomolecular Sciences (DiSFeB), University of Milan, Via Pascal 36, 20133, Milan, Italy
| | - Donatella Taramelli
- Department of Pharmacological & Biomolecular Sciences (DiSFeB), University of Milan, Via Pascal 36, 20133, Milan, Italy
| | - Isabella Castiglioni
- Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), Via F.Cervi 93, 20090, Segrate, Milan, Italy
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